Personal Allowance not taken into account

Hi, I've just filled in my self assessment, and the it's saying I owe an additional ~£4,500, even though I paid tax through PAYE. Looking at the detailed calculation, it looks like my personal allowance hasn't been deducted, so I'm being charged an extra 40% of my PA (since my salary falls into the 40% bracket). Am I supposed to deduct this from the "income from P60" section myself? I don't see any notes on this, or any other section to enter PA or tax code. Thanks, Peter.

Hi,

You should receive the full Personal Allowance unless your income is over £100,000. For every £2 you earn above this you lose £1 of Personal Allowance. If you have included the tax that you paid from your employment and you should have the Personal Allowance, please contact our helpline 72 hours after submitting the return and we can view the calculation.

Self Assessment: general enquiries

Thank you.